X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FJPredClient.java;h=65847e6db6a06e2d9f80ed70fde474f5c8997295;hb=0935f3c68446aa5cd3a928295a0c5ea78f303648;hp=1a96464cf455083f7dcdd0c876b896c91901f8cd;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git

diff --git a/src/jalview/ws/jws1/JPredClient.java b/src/jalview/ws/jws1/JPredClient.java
index 1a96464..65847e6 100644
--- a/src/jalview/ws/jws1/JPredClient.java
+++ b/src/jalview/ws/jws1/JPredClient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,18 +20,28 @@
  */
 package jalview.ws.jws1;
 
+import jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
+
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.util.*;
+import java.util.Hashtable;
 
-import javax.swing.*;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
 
-import ext.vamsas.*;
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.util.MessageManager;
+import ext.vamsas.Jpred;
+import ext.vamsas.JpredServiceLocator;
+import ext.vamsas.JpredSoapBindingStub;
+import ext.vamsas.ServiceHandle;
 
 public class JPredClient extends WS1Client
 {
@@ -144,7 +154,9 @@ public class JPredClient extends WS1Client
     {
       if (!msa && msf.length > 1)
       {
-        throw new Error(MessageManager.getString("error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_error_multiple_single_sequence_prediction_jobs_not_supported"));
       }
 
       String altitle = getPredictionName(WebServiceName) + " for "
@@ -226,7 +238,7 @@ public class JPredClient extends WS1Client
 
     SequenceI seq = msf[0];
 
-    String altitle = "JNet prediction on " + seq.getName()
+    String altitle = "JPred prediction on " + seq.getName()
             + " using alignment from " + title;
 
     wsInfo.setProgressText("Job details for MSA based prediction (" + title
@@ -263,7 +275,7 @@ public class JPredClient extends WS1Client
     wsInfo.setProgressText("Job details for prediction on sequence :\n>"
             + seq.getName() + "\n"
             + AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) + "\n");
-    String altitle = "JNet prediction for sequence " + seq.getName()
+    String altitle = "JPred prediction for sequence " + seq.getName()
             + " from " + title;
 
     Hashtable SequenceInfo = jalview.analysis.SeqsetUtils
@@ -284,14 +296,15 @@ public class JPredClient extends WS1Client
   private WebserviceInfo setWebService()
   {
     WebServiceName = "JNetWS";
-    WebServiceJobTitle = MessageManager.getString("label.jnet_secondary_structure_prediction");
+    WebServiceJobTitle = MessageManager
+            .getString("label.jnet_secondary_structure_prediction");
     WebServiceReference = "\"Cuff J. A and Barton G.J (2000) Application of "
             + "multiple sequence alignment profiles to improve protein secondary structure prediction, "
             + "Proteins 40:502-511\".";
     WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";
 
     WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,
-            WebServiceReference);
+            WebServiceReference, true);
 
     return wsInfo;
   }
@@ -310,13 +323,21 @@ public class JPredClient extends WS1Client
 
     } catch (Exception ex)
     {
-      JOptionPane.showMessageDialog(Desktop.desktop,
-    		  MessageManager.formatMessage("label.secondary_structure_prediction_service_couldnt_be_located", new String[]{WebServiceName,WsURL}),
-    		  MessageManager.getString("label.internal_jalview_error"),
-              JOptionPane.WARNING_MESSAGE);
-      wsInfo.setProgressText(MessageManager.formatMessage("label.secondary_structure_prediction_service_couldnt_be_located", new String[]{WebServiceName,WsURL})
-    		  + "\n"
-              + ex.getMessage());
+      JvOptionPane
+              .showMessageDialog(
+                      Desktop.desktop,
+                      MessageManager
+                              .formatMessage(
+                                      "label.secondary_structure_prediction_service_couldnt_be_located",
+                                      new String[] { WebServiceName, WsURL }),
+                      MessageManager
+                              .getString("label.internal_jalview_error"),
+                      JvOptionPane.WARNING_MESSAGE);
+      wsInfo.setProgressText(MessageManager
+              .formatMessage(
+                      "label.secondary_structure_prediction_service_couldnt_be_located",
+                      new String[] { WebServiceName, WsURL })
+              + "\n" + ex.getMessage());
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
 
     }
@@ -324,6 +345,7 @@ public class JPredClient extends WS1Client
     return server;
   }
 
+  @Override
   public void attachWSMenuEntry(JMenu wsmenu, final ServiceHandle sh,
           final AlignFrame af)
   {
@@ -331,6 +353,7 @@ public class JPredClient extends WS1Client
     method.setToolTipText(sh.getEndpointURL());
     method.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         AlignmentView msa = af.gatherSeqOrMsaForSecStrPrediction();